Project description:Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) and genotyping in peripheral blood mononuclear cells from 13 individuals. We mapped chromatin accessibility QTLs (caQTLs) in each immune cell type and sub-type in a subset of 10 samples of European genetic ancestry.
Project description:Recent studies have uncovered thousands of long non-coding RNAs (lncRNAs) in human pancreatic β cells. β cell lncRNAs are often cell type specific and exhibit dynamic regulation during differentiation or upon changing glucose concentrations. Although these features hint at a role of lncRNAs in β cell gene regulation and diabetes, the function of β cell lncRNAs remains largely unknown. In this study, we investigated the function of β cell-specific lncRNAs and transcription factors using transcript knockdowns and co-expression network analysis. This revealed lncRNAs that function in concert with transcription factors to regulate β cell-specific transcriptional networks. We further demonstrate that the lncRNA PLUTO affects local 3D chromatin structure and transcription of PDX1, encoding a key β cell transcription factor, and that both PLUTO and PDX1 are downregulated in islets from donors with type 2 diabetes or impaired glucose tolerance. These results implicate lncRNAs in the regulation of β cell-specific transcription factor networks.
Project description:Inherited TTC7A loss of function mutations causes intestinal and immune deficiency. TTC7A is expressed in hematopoietic and epithelial cells however its cellular function remains poorly understood. In this work we provided evidence that TTC7A is an intrinsic nucleus factor. In an attempt to link the function of TTC7A in chromatin compaction, histone modifications and general transcriptional regulation we undertook to map the observed interaction of TTC7A to chromatin genome-wide by ChiP-Seq of Flag-tagged WT_TTC7A expressed in B lymphoblastoid cell lines using two anti-Flag antibodies (hereafter IP-Flag1 and IP-Flag2).
Project description:Post-translational modifications of histones determines cell lineage- or signal-specific gene expression. Depending on the type and combination of modifications, histones bind to functionally distinct effector proteins ('readers') that control gene activation or silencing. The current pharmacological modulation of the epigenome aims to control gene expression by regulation of the enzymes that catalyze post-translational histone modifications. Here we present a novel pharmacological approach that targets gene expression by interfering with the function of histone ?readers?. We describe the impact of a synthetic compound that selectively occupies the acetylated histone-binding pocket of the Bromodomain and Extra Terminal domain (BET) family of proteins and prevents their interaction with acetylated histones. The bromodomain blocking compound suppresses the expression of a specific subset of key inflammatory genes in activated macrophages and confers protection against LPS-induced septic shock in vivo. Our findings suggest that small molecules specifically targeting histone 'readers' can serve as a new generation of drugs to treat immune diseases. Microarray, ChIP-qPCR and ChIP-seq examination of control, 1H LPS stimulated bone-marrow-derived macrophages in the presence/absence of acetylated histone mimic in mouse.
Project description:This study aims to dissect gene-environment interactions on gene expression and regulation in immune cells using scRNA-seq data from 120 donors being stimulated with 3 pathogens, for 2 different timepoints. More specifically, we identified context- and cell-type-specific eQTLs and co-expression QTLs in PBMCs.
| EGAS00001005376 | EGA
Project description:Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System